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800 results • Page 3 of 16
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2
votes
5
replies
491
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 2 days ago by 43k • written 8 days ago by • 0
1
vote
3
replies
432
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE BAM SAM flag paired-end
3 days ago by kalavattam ▴ 190
1
vote
2
replies
265
views
How to interpret infinite odds ratio?
statistics
2 days ago by Lukas • 0
1
vote
2
replies
178
views
Duplicated sequence samtools
bowtie2 samtools
updated 3 days ago by 142k • written 3 days ago by • 0
0
votes
0
replies
104
views
reference-free assembly error assessment tools
assembly
3 days ago by lagartija ▴ 160
2
votes
4
replies
292
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
2 days ago by Esraa • 0
2
votes
0
replies
141
views
Herald: The Biostar Herald for Monday, May 13, 2024
herald
3 days ago by Biostar 2.8k
0
votes
1
reply
142
views
Splitting Seurat object by sample layers
seurat
updated 3 days ago by 43k • written 3 days ago by ▴ 10
0
votes
4
replies
257
views
Galaxy StringTie error
stringtie galaxy
2 days ago by trkfs • 0
0
votes
0
replies
103
views
dbNSFP sift scores integration
SIFT VEP dbNSFP
3 days ago by atariw ▴ 10
0
votes
1
reply
153
views
Mouse ribosome sequences in fasta format
fasta mm10 rRNA
updated 3 days ago by 142k • written 4 days ago by ▴ 100
1
vote
4
replies
341
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus annotation assembly genome
updated 2 days ago by 8.6k • written 3 days ago by ▴ 30
0
votes
1
reply
161
views
consensus sequence calling
consensus
updated 3 days ago by ★ 2.5k • written 3 days ago by • 0
0
votes
3
replies
190
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat single-cell scRNA-seq R
updated 3 days ago by 43k • written 3 days ago by • 0
3
votes
2
replies
277
views
imputation through beagle
panel beagle reference imputation
3 days ago by analyst ▴ 50
0
votes
0
replies
88
views
Empty kernel in SEACells model
single-cell scanpy seacells python anndata
3 days ago by JACKY ▴ 140
0
votes
1
reply
530
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
updated 3 days ago by ▴ 300 • written 27 days ago by • 0
3
votes
1
reply
216
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair samtools alignment
updated 3 days ago by ▴ 300 • written 8 days ago by ▴ 40
0
votes
0
replies
101
views
Reference panel of normals for ensembl named refgenome
Mutect2
4 days ago by gernophil ▴ 80
1
vote
0
replies
96
views
Producing sequence for splicing isoforms
isoform rMATs splicing alternative SplAdder
4 days ago by tomas4482 ▴ 400
2
votes
6
replies
380
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
3
votes
2
replies
189
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 4 days ago by 82k • written 4 days ago by • 0
0
votes
1
reply
157
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence university assembly protein genomics
updated 4 days ago by 8.5k • written 4 days ago by • 0
0
votes
1
reply
245
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 3 days ago by 43k • written 7 days ago by • 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 2 days ago by • 0 • written 4.8 years ago by ▴ 60
0
votes
1
reply
194
views
Generating .bed file and .map file for polyploid vcf file through plink
bed polyploid map plink
updated 4 days ago by 10k • written 9 days ago by ▴ 50
0
votes
0
replies
109
views
lncRNA
tcga lncrna
4 days ago by jain72744 ▴ 10
0
votes
1
reply
242
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA RNA-seq Nomalization Microarray
updated 4 days ago by ★ 1.2k • written 7 days ago by ▴ 10
2
votes
5
replies
567
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 4 days ago by ▴ 40 • written 13 days ago by ▴ 30
1
vote
2
replies
358
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq limma RNA-seq removeBatchEffect batch-effect
updated 3 days ago by 43k • written 4 days ago by • 0
2
votes
1
reply
258
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
updated 4 days ago by ▴ 210 • written 6 days ago by ▴ 10
0
votes
2
replies
209
views
Output file of samtools flagstat empty
samtools-flagstat
updated 4 days ago by 6.4k • written 4 days ago by • 0
2
votes
8
replies
375
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 4 days ago by 161k • written 4 days ago by ▴ 100
0
votes
0
replies
128
views
News: Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore RNAseq
5 days ago by carlopecoraro2 ★ 2.5k
0
votes
1
reply
230
views
input file in rmats
rmats
updated 5 days ago by ▴ 140 • written 7 days ago by • 0
3
votes
3
replies
358
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 3 days ago by ▴ 140 • written 6 days ago by • 0
6
votes
7
replies
385
views
Longest transcript variant per gene
transcript longest variant orthofinder
4 days ago by sansan_96 ▴ 90
2
votes
3
replies
276
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio Cibersort R
3 days ago by Azra ▴ 10
2
votes
1
reply
232
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 5 days ago by 161k • written 6 days ago by ▴ 70
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 5 days ago by • 0 • written 5.7 years ago by ▴ 20
0
votes
4
replies
396
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days ago by beginner123 • 0
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated 5 days ago by • 0 • written 6.5 years ago by ▴ 130
0
votes
2
replies
229
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated java.nio.bufferunderflowexception haplotypecaller bqsr
4 days ago by analyst ▴ 50
0
votes
6
replies
419
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf genomics plink
updated 3 days ago by 43k • written 6 days ago by • 0
0
votes
11
replies
533
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
4 days ago by Tuck898 • 0
3
votes
3
replies
280
views
what is another word for a BLAST "hit"?
blast alignment
6 days ago by dec986 ▴ 380
0
votes
1
reply
203
views
extract viral protein of interest from 10k whole viral genomes
nBLAST viral-genome
updated 6 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
164
views
Marker Features variance by cluster, sample, and treatment group
Seurat scATAC-seq ArchR
updated 6 days ago by 43k • written 6 days ago by • 0
1
vote
3
replies
283
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk vcf liftover
updated 6 days ago by 43k • written 6 days ago by ▴ 260
2
votes
9
replies
694
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 2 days ago by 161k • written 9 days ago by • 0
800 results • Page 3 of 16
Recent Votes
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
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Recent Replies
Answer: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input? by Pierre Lindenbaum 161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem by Pierre Lindenbaum 161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences? by DGTool ▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by b.contreras.moreira ▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input? by LucisTheFather • 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
thank you
Comment: How to extract cells of different species after mapping with combined genome? by Tony • 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Nyksubuz ▴ 20
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test by Nyksubuz ▴ 20
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 20
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
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